M. Roach, Bradley J. Hart, Sarah J. Beecroft, B. Papudeshi, Laura K. Inglis, Susanna R. Grigson, Vijini Mallawaarachchi, G. Bouras, Rob A. Edwards
{"title":"Koverage: Read-coverage analysis for massive\u0000(meta)genomics datasets","authors":"M. Roach, Bradley J. Hart, Sarah J. Beecroft, B. Papudeshi, Laura K. Inglis, Susanna R. Grigson, Vijini Mallawaarachchi, G. Bouras, Rob A. Edwards","doi":"10.21105/joss.06235","DOIUrl":"https://doi.org/10.21105/joss.06235","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"41 18","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140425405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
S. M. Garrison, Michael D. Hunter, Xuanyu Lyu, Jonathan D. Trattner, S. A. Burt
{"title":"BGmisc: An R Package for Extended Behavior Genetics\u0000Analysis","authors":"S. M. Garrison, Michael D. Hunter, Xuanyu Lyu, Jonathan D. Trattner, S. A. Burt","doi":"10.21105/joss.06203","DOIUrl":"https://doi.org/10.21105/joss.06203","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"41 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140435029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"stemflow: A Python Package for Adaptive Spatio-Temporal\u0000Exploratory Model","authors":"Yangkang Chen, Zhongru Gu, Xiangjiang Zhan","doi":"10.21105/joss.06158","DOIUrl":"https://doi.org/10.21105/joss.06158","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"21 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140435998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
N. Richart, G. Anciaux, E. Gallyamov, L. Frérot, David Kammer, Mohit Pundir, Marco Vocialta, A. C. Ramos, Mauro Corrado, Philip Müller, Fabian Barras, Shenghan Zhang, Roxane Ferry, Shad Durussel, J-F Molinari
the heart of modern research in mechanics of materials. For example, the buildup and release of elastic energy at geological fault is what causes earthquakes, and the intricate details of the slip zone, the propagation of slip fronts and waves radiated through the various geological media are still active areas of research
{"title":"Akantu: an HPC finite-element library for contact and\u0000dynamic fracture simulations","authors":"N. Richart, G. Anciaux, E. Gallyamov, L. Frérot, David Kammer, Mohit Pundir, Marco Vocialta, A. C. Ramos, Mauro Corrado, Philip Müller, Fabian Barras, Shenghan Zhang, Roxane Ferry, Shad Durussel, J-F Molinari","doi":"10.21105/joss.05253","DOIUrl":"https://doi.org/10.21105/joss.05253","url":null,"abstract":"the heart of modern research in mechanics of materials. For example, the buildup and release of elastic energy at geological fault is what causes earthquakes, and the intricate details of the slip zone, the propagation of slip fronts and waves radiated through the various geological media are still active areas of research","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140440642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mengqi Zhao, Zarrar Khan, K. Dorheim, Chris Vernon
electricity
电
{"title":"helios: An R package to process heating and cooling\u0000degrees for GCAM","authors":"Mengqi Zhao, Zarrar Khan, K. Dorheim, Chris Vernon","doi":"10.21105/joss.06033","DOIUrl":"https://doi.org/10.21105/joss.06033","url":null,"abstract":"electricity","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"15 s1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140439859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Summary Stokesian Dynamics (Brady & Bossis, 1988) is a microhydrodynamic, low Reynolds number approach to modelling the movement of suspensions of particles in fluids, which considers the interaction of particles with each other against a Newtonian background solvent. It is typically chosen for its suitability for three-dimensional simulation with low calculation and time penalty. In the most basic case, Stokes’ law states that a single sphere of radius 𝑎 , travelling with a velocity 𝑈 in an unbounded Newtonian fluid of viscosity 𝜇 , in a low Reynolds number regime, experiences a drag force, 𝐹 , of 𝐹 = −6𝜋𝜇𝑎𝑈 . Stokesian Dynamics, at its heart, is an extension of this linear relationship between the force acting on a particle and the velocity at which it travels. As a method, it is adaptable and continues to be used in the field, providing interesting insight into the behaviour of particle suspensions. Validations with experiments have shown it to provide results within acceptable error. The
{"title":"Stokesian Dynamics in Python","authors":"A. Townsend","doi":"10.21105/joss.06011","DOIUrl":"https://doi.org/10.21105/joss.06011","url":null,"abstract":"Summary Stokesian Dynamics (Brady & Bossis, 1988) is a microhydrodynamic, low Reynolds number approach to modelling the movement of suspensions of particles in fluids, which considers the interaction of particles with each other against a Newtonian background solvent. It is typically chosen for its suitability for three-dimensional simulation with low calculation and time penalty. In the most basic case, Stokes’ law states that a single sphere of radius 𝑎 , travelling with a velocity 𝑈 in an unbounded Newtonian fluid of viscosity 𝜇 , in a low Reynolds number regime, experiences a drag force, 𝐹 , of 𝐹 = −6𝜋𝜇𝑎𝑈 . Stokesian Dynamics, at its heart, is an extension of this linear relationship between the force acting on a particle and the velocity at which it travels. As a method, it is adaptable and continues to be used in the field, providing interesting insight into the behaviour of particle suspensions. Validations with experiments have shown it to provide results within acceptable error. The","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"81 1‐2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140440052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frederik L. Johansen, A. Anker, Ulrik Friis-Jensen, Erik B. Dam, Kirsten M Ø Jensen, Raghavendra Selvan
{"title":"A GPU-Accelerated Open-Source Python Package for\u0000Calculating Powder Diffraction, Small-Angle-, and Total Scattering with\u0000the Debye Scattering Equation","authors":"Frederik L. Johansen, A. Anker, Ulrik Friis-Jensen, Erik B. Dam, Kirsten M Ø Jensen, Raghavendra Selvan","doi":"10.21105/joss.06024","DOIUrl":"https://doi.org/10.21105/joss.06024","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"150 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140449285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andrew R. McCluskey, Alexander G. Squires, Josh Dunn, Samuel W. Coles, Benjamin J. Morgan
{"title":"kinisi: Bayesian analysis of mass transport from\u0000molecular dynamics simulations","authors":"Andrew R. McCluskey, Alexander G. Squires, Josh Dunn, Samuel W. Coles, Benjamin J. Morgan","doi":"10.21105/joss.05984","DOIUrl":"https://doi.org/10.21105/joss.05984","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"24 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140450457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"growR: R Implementation of the Vegetation Model\u0000ModVege","authors":"Kevin P. Kramer, Pierluigi Calanca","doi":"10.21105/joss.06260","DOIUrl":"https://doi.org/10.21105/joss.06260","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"659 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139835786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"growR: R Implementation of the Vegetation Model\u0000ModVege","authors":"Kevin P. Kramer, Pierluigi Calanca","doi":"10.21105/joss.06260","DOIUrl":"https://doi.org/10.21105/joss.06260","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"36 18","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139775943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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